Toggle navigation
Peak Browser
Enrichment Analysis
Diff Analysis
Target Genes
Colocalization
Publications
Docs
Search
Go
Find By ID
Visualize
Install and launch IGV before selecting data to visualize
For hg38
BigWig
Peak-call (q < 1E-05)
Peak-call (q < 1E-10)
Peak-call (q < 1E-20)
For hg19
BigWig
Peak-call (q < 1E-05)
Peak-call (q < 1E-10)
Peak-call (q < 1E-20)
Error connecting to IGV?
Analyze
For hg38
Colocalization
Target Genes (TSS ± 1kb)
Target Genes (TSS ± 5kb)
Target Genes (TSS ± 10kb)
For hg19
Colocalization
Target Genes (TSS ± 1kb)
Target Genes (TSS ± 5kb)
Target Genes (TSS ± 10kb)
Download
For hg38
BigWig
Peak-call (q < 1E-05)
Peak-call (q < 1E-10)
Peak-call (q < 1E-20)
For hg19
BigWig
Peak-call (q < 1E-05)
Peak-call (q < 1E-10)
Peak-call (q < 1E-20)
Link Out
Sequence Read Archive
DBCLS SRA
NCBI SRA
ENA
Antigen: HDAC1
wikigenes
PDBj
CellType: MIA Paca-2
ATCC
MeSH
RIKEN BRC
Variation
TogoVar
SRX9187412
GSM4802504: MiaPaCa2 NTC Santa Cruz, rep1; Homo sapiens; ChIP-Seq
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
TFs and others
Antigen
HDAC1
Cell type
Cell type Class
Pancreas
Cell type
MIA Paca-2
Primary Tissue
Pancreas
Tissue Diagnosis
Carcinoma
Attributes by original data submitter
Sample
source_name
MiaPaCa2 cells
cell line
MiaPaCa2
treatment
Scrambled non-targeting sgRNA
chip antibody
Santa Cruz Biotechnologies sc-81598 HDAC1(10E2)
Sequenced DNA Library
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP-seq protocol Myers Lab: https://www.encodeproject.org/documents/73c95206-fc02-41ea-93e0-a929a6939aaf/ ChIP-seq protocol Myers Lab; used antibodies: Santa Cruz Biotechnologies sc-81598 HDAC1(10E2) and Invitrogen HDAC1 Polyclonal Antibody PA1-860
Sequencing Platform
instrument_model
Illumina NovaSeq 6000
Where can I get the processing logs?
Read processing pipeline
log
hg38
Number of total reads
72279796
Reads aligned (%)
87.5
Duplicates removed (%)
11.6
Number of peaks
5958 (qval < 1E-05)
hg19
Number of total reads
72279796
Reads aligned (%)
86.8
Duplicates removed (%)
13.0
Number of peaks
5327 (qval < 1E-05)
Base call quality data from
DBCLS SRA